Is is possible that you have your rare earth magnets spread too far apart on your fan? I generally think that having the ends of your stirbar match close to the middle of each rare earth magnet will give the best attraction. Unfortunately, if the magnets are glued, it can be a PITA to fix. Measure the distance between the centers of the rare earth magnets; is it close to your 1" stirbar?
Are you using one hd magnet or two? If two, are they spit in half?
A couple ideas to test that might be easier would be distance between stirbar and rare earth magnets. Using non-metallic medium (thin plastic, cardboard, cardstock, paper, etc), try spacing a little further away (place the paper on your stirplate and put your flask on top of that). See if further distance helps or hurts. If it hurts, then try getting things closer. Move your fan up closer to the project box so the distance to the stirbar is reduced. See if it helps or hurts.
Homemade stirplates are cool but they definitely take a little trial-and-error to get the bugs out. The good news is that once you get your bugs out, it should remain good until the fan dies